Statistical Genetics Seminar

Spring 2005

“Experimental Genetics with Model Organisms”

 

Here are some papers that were suggested by some colleagues.  Below some of the papers I included some comments made when the paper was suggested.

 

1.      Broman, K.  Review of statistical methods for QTL mapping in experimental crosses.  Lab Animal 30(7):44–52, 2001.

·        A well-written review aimed at non-statisticians.

2.      Lander ES, Botstein D, Mapping Mendelian factors underlying quantitative traits using RFLP linkage maps, Genetics. 1989; 121(1):185-199.

·        A “seminal” paper

·        A classic with many ideas (EM algorithm, selective genotyping, genome-wide thresholds corrected for multiple comparisons).  Must read.

3.      Kong A, Wright F, Asymptotic theory for gene-mapping PNAS; 1994;
91(21):9705-9709.

·        An under-appreciated paper, very terse, but has a very important, very general result that deserves greater attention.

4.      Broman KW, The genomes of recombinant inbred lines.  Genetics. 2005;
169(2):1133-46.

·        A new paper that does the math for recombinant inbred lines, and can be considered the rightful decendant of a classic paper by Haldane and Waddington.  Very important for future developments in experimental crosses.

5.      Dupuis J, Siegmund D, Statistical methods for mapping quantitative
trait loci from a dense set of markers, Genetics, 1999; 151(1):373-386.

·        Dupuis and Siegmund (1999) has a lot of statistically sound ideas for
genetic mapping.

6.      Churchill GA, Doerge RW, Empirical threshold values for quantitative
trait mapping Genetics, 1994; 138(3):963-971.

·        Proposes a simple idea with far-reaching consequences.

7.      Broman KW, Speed TP.  A model selection approach for the identification of quantitative trait loci in experimental crosses.  J Roy Stat Soc B 64:641-656, 731-775

8.      Sen S, Churchill GA.  A Statistical Framework for Quantitative Trait Mapping.  Genetics 159: 371–387 (2001).

9.      Broman K.  Mapping Quantitative Trait Loci in the Case of a Spike in the Phenotype Distribution.  Genetics 163: 1169–1175 (2003)

10.  Sen S, Satagopan JM ,Churchill GA.  QTL Study Design from an Information Perspective. Genetics, in press. http://www.biostat.ucsf.edu/sen/research.html

  • Looks at the statistical design of QTL studies including selective genotyping, selective phenotyping, and missing data.

11.  Schadt EE, Monks SA et al.  Genetics of Gene Exprsesion surveyed in maize, mouse, and man.  Nature 2003

  • Covered in StatGen seminar recently?

12.  Brem RB, Yvert G, Clinton R, Kruglyak L. (2002) Genetic dissection of
transcriptional regulation in budding yeast. Science, 296: 752-755.

13.  Frank H. Shaw, Daniel E. L. Promislow, Marc Tatar, Kimberly A. Hughes, and
Charles J. Geyer.  Toward Reconciling Inferences Concerning Genetic Variation in
 Senescence in Drosophila melanogaster     Genetics 1999 152: 553-566.

14.  Fridman et al (2004) Zooming in on a quantitative trait for tomato yield
using interspecific introgressions. Science 305:1786-1789.

  •  It would be interesting to contrast this paper to similar work in drosophila, probably by Trudy Mackay's group. Searched Genetics for Trudy Mackay papers since 1998 -- 28 found, so did not check them all, but several could be quite interesting.

15.  Steinmetz, L.M., Sinha, H., Richards, D.R., Spiegelman, J.I., Oefner,
P.J., McCusker, J.H., Davis, R.W., (2002). Dissecting the architecture
of a quantitative trait locus in yeast. Nature, 416: 326-330

 

Classics that involve statistics:

1.      Mendel, J. Gregor (1866) Experiments in plant hybridization.
Verhandlungen des naturforschenden Vereines in Brünn. 4: 3-47.

2.      Sturtevant (1913) ... don't know exact reference, but this is the first
genetic map based on recombination in Drosophila.

3.      Luria, S.E. and Delbrück M. (1943) Mutations of bacteria from virus
sensitivity to virus resistance. Genetics 28: 491